Melopsittacus undulatus isolate bMelUnd1 chromosome 28, bMelUnd1.mat.Z, whole genome shotgun sequence.
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Psittaciformes; Psittaculidae; Melopsittacus.
REFSEQ INFORMATION: The reference sequence is identical to\nCM022659.1.\nAssembly name: bMelUnd1.mat.Z\nThe genomic sequence for this RefSeq record is from the\nwhole-genome assembly released by the G10K on 2020/04/13. The\noriginal whole-genome shotgun project has the accession\nJAAVWG000000000.1.\n\n##Genome-Assembly-Data-START##\nAssembly Provider :: G10K\nAssembly Date :: 24-FEB-2020\nAssembly Method :: TrioCanu v. 1.8; purge_dups v. 1.0.0;\n Scaff 10x v. 4.1.0; Bionano solve v.\n 3.2.1_04122018; Salsa2 HiC v. 2.2; Arrow\n polishing and gap filling v.\n smrtlink_6.0.0.47841; Longranger Align v.\n 2.2.2; Freebayes v. 1.3.1; gEVAL manual\n curation v. 2020-02-24; VGP assembly\n pipeline v. 1.6\nAssembly Name :: bMelUnd1.mat.Z\nDiploid :: Principal pseudohaplotype\nGenome Representation :: Full\nExpected Final Version :: No\nGenome Coverage :: 61.11x\nSequencing Technology :: PacBio Sequel I CLR; Illumina NovaSeq;\n Arima Genomics Hi-C; Bionano Genomics DLS\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI\nAnnotation Status :: Full annotation\nAnnotation Name :: Melopsittacus undulatus Annotation\n Release 104\nAnnotation Version :: 104\nAnnotation Pipeline :: NCBI eukaryotic genome annotation\n pipeline\nAnnotation Software Version :: 8.4\nAnnotation Method :: Best-placed RefSeq; Gnomon\nFeatures Annotated :: Gene; mRNA; CDS; ncRNA\n##Genome-Annotation-Data-END##
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
transfer RNA leucine (anticodon CAA); Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
transfer RNA glutamic acid (anticodon CUC); Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
Derived by automated computational analysis using gene prediction method: Gnomon.
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 9 Proteins, and 56% coverage of the annotated genomic feature by RNAseq alignments
transfer RNA asparagine (anticodon GUU); Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
transfer RNA threonine (anticodon UGU); Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
transfer RNA leucine (anticodon AAG); Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
transfer RNA valine (anticodon AAC); Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
transfer RNA proline (anticodon UGG); Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 mRNA, 21 Proteins, and 97% coverage of the annotated genomic feature by RNAseq alignments, including 1 sample with support for all annotated introns
transfer RNA lysine (anticodon CUU); Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
transfer RNA valine (anticodon CAC); Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: inserted 2 bases in 1 codon; Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 20 Proteins, and 90% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
The sequence of the model RefSeq protein was modified relative to this genomic sequence to represent the inferred CDS: inserted 2 bases in 1 codon; Derived by automated computational analysis using gene prediction method: Gnomon.
LOW QUALITY PROTEIN: E3 ubiquitin-protein ligase TRIM41-like
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 4 mRNAs, 32 ESTs, 24 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
receptor of activated protein C kinase 1
E3 ubiquitin-protein ligase TRIM58-like, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 10 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 1 sample with support for all annotated introns
E3 ubiquitin-protein ligase TRIM58-like, transcript variant X3
E3 ubiquitin-protein ligase TRIM58-like, transcript variant X4
E3 ubiquitin-protein ligase TRIM58-like, transcript variant X5
E3 ubiquitin-protein ligase TRIM58-like, transcript variant X6
E3 ubiquitin-protein ligase TRIM58-like, transcript variant X2
E3 ubiquitin-protein ligase TRIM58-like isoform X1
E3 ubiquitin-protein ligase TRIM58-like isoform X3
E3 ubiquitin-protein ligase TRIM58-like isoform X4
E3 ubiquitin-protein ligase TRIM58-like isoform X5
E3 ubiquitin-protein ligase TRIM58-like isoform X6
E3 ubiquitin-protein ligase TRIM58-like isoform X2
E3 ubiquitin-protein ligase TRIM58-like, transcript variant X7
E3 ubiquitin-protein ligase TRIM58-like isoform X7
zinc finger protein interacting with ribonucleoprotein K-like
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 22% coverage of the annotated genomic feature by RNAseq alignments
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 Protein, and 98% coverage of the annotated genomic feature by RNAseq alignments
abhydrolase domain containing 16A, phospholipase
coiled-coil alpha-helical rod protein 1-like
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 5 samples with support for all annotated introns
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 Protein, and 66% coverage of the annotated genomic feature by RNAseq alignments, including 5 samples with support for all annotated introns
mediator of DNA damage checkpoint protein 1
The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: deleted 1 base in 1 codon; Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 7 ESTs, 184 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
The sequence of the model RefSeq protein was modified relative to this genomic sequence to represent the inferred CDS: deleted 1 base in 1 codon; Derived by automated computational analysis using gene prediction method: Gnomon.
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 EST, 1 Protein, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 EST, 12 Proteins, and 97% coverage of the annotated genomic feature by RNAseq alignments
uncharacterized LOC117437808, transcript variant X1
uncharacterized LOC117437808, transcript variant X7
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 3 samples with support for all annotated introns
uncharacterized LOC117437808, transcript variant X2
uncharacterized LOC117437808, transcript variant X3
uncharacterized LOC117437808, transcript variant X5
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns
uncharacterized LOC117437808, transcript variant X6
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
uncharacterized LOC117437808, transcript variant X4
class I histocompatibility antigen, F10 alpha chain-like, transcript variant X6
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 18 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns
class I histocompatibility antigen, F10 alpha chain-like, transcript variant X3
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 297 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 5 samples with support for all annotated introns
class I histocompatibility antigen, F10 alpha chain-like, transcript variant X4
class I histocompatibility antigen, F10 alpha chain-like, transcript variant X5
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 297 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns
class I histocompatibility antigen, F10 alpha chain-like, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 298 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns
class I histocompatibility antigen, F10 alpha chain-like, transcript variant X2
class I histocompatibility antigen, F10 alpha chain-like, transcript variant X7
class I histocompatibility antigen, F10 alpha chain-like isoform X6
class I histocompatibility antigen, F10 alpha chain-like isoform X1
class I histocompatibility antigen, F10 alpha chain-like isoform X2
class I histocompatibility antigen, F10 alpha chain-like isoform X3
class I histocompatibility antigen, F10 alpha chain-like isoform X4
class I histocompatibility antigen, F10 alpha chain-like isoform X5
class I histocompatibility antigen, F10 alpha chain-like isoform X7
WD repeat domain 46, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 6 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 1 sample with support for all annotated introns
WD repeat domain 46, transcript variant X2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 Protein, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 3 samples with support for all annotated introns
WD repeat-containing protein 46 isoform X1
WD repeat-containing protein 46 isoform X2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 mRNA, 36 ESTs, 13 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 7 samples with support for all annotated introns
VPS52 subunit of GARP complex, transcript variant X2
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 Protein, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
VPS52 subunit of GARP complex, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 2 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
VPS52 subunit of GARP complex, transcript variant X3
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 Protein, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 1 sample with support for all annotated introns
vacuolar protein sorting-associated protein 52 homolog isoform X2
vacuolar protein sorting-associated protein 52 homolog isoform X3
vacuolar protein sorting-associated protein 52 homolog isoform X1
ring finger protein 1, transcript variant X1
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 6 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
ring finger protein 1, transcript variant X3
Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 16 Proteins, and 97% coverage of the annotated genomic feature by RNAseq alignments
ring finger protein 1, transcript variant X2
E3 ubiquitin-protein ligase RING1 isoform X1
E3 ubiquitin-protein ligase RING1 isoform X3
E3 ubiquitin-protein ligase RING1 isoform X2
The sequence of the model RefSeq transcript was modified relative to this genomic sequence to represent the inferred CDS: inserted 2 bases in 1 codon; deleted 1 base in 1 codon; Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 1 Protein, and 72% coverage of the annotated genomic feature by RNAseq alignments, including 2 samples with support for all annotated introns
The sequence of the model RefSeq protein was modified relative to this genomic sequence to represent the inferred CDS: inserted 2 bases in 1 codon; deleted 1 base in 1 codon; Derived by automated computational analysis using gene prediction method: Gnomon.
LOW QUALITY PROTEIN: zinc transporter SLC39A7